Identification of alternatively spliced transcripts using a proteomic informatics approach

Methods Mol Biol. 2011;696:319-26. doi: 10.1007/978-1-60761-987-1_20.


We present the protocol for the identification of alternatively spliced peptide sequences from tandem mass spectrometry datasets searched using X!Tandem against our modified ECgene resource with all potential translation products and then matched with the Michigan Peptide to Protein Integration (MPPI) scheme. This approach is suitable for human and mouse datasets. Application of the method is illustrated with a study of the Kras activation-Ink4/Arf deletion mouse model of human pancreatic ductal adenocarcinoma.

MeSH terms

  • Alternative Splicing / genetics*
  • Base Sequence
  • Databases, Genetic
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Informatics / methods*
  • Mass Spectrometry
  • Molecular Sequence Annotation
  • Pancreatic Neoplasms / genetics
  • Peptides / analysis
  • Proteomics / methods*
  • RNA, Messenger / analysis*
  • RNA, Messenger / genetics*
  • Reproducibility of Results
  • Sequence Analysis, Protein


  • Peptides
  • RNA, Messenger